I'm using a WiFi Shield with a Mega2560. I am now at the stage where I can design a PCB, but in order to do so I need a better understanding of how the Mega interacts with the WiFi Shield. I'm looking to take the AT32UC3A1256 chip from the Shield and put it on the PCB, but I don't know if I need to program the chip itself, or if I only need to program the Atmel chip on the Arduino and that will send necessary instructions to the AT32UC3A1256. Any thoughts?

To duplicate the functionality of the WiFi Shield you will need to install the firmware in the AT32 processor. You should be able to find the firmware among the design documents. See links at http://arduino.cc/en/Main/ArduinoWiFiShield

Ah, so the AT32 only needs to store its firmware to interact with the Arduino? More specifically, when I have the WiFi Shield connected to the Mega2560, the entire program is stored to the processor on the Mega, and that then talks to the AT32 (which has the firmware loaded on ahead of time)?

Ah, so the AT32 only needs to store its firmware to interact with the Arduino? More specifically, when I have the WiFi Shield connected to the Mega2560, the entire program is stored to the processor on the Mega, and that then talks to the AT32 (which has the firmware loaded on ahead of time)?

Yes. Once the AT32 has its firmware it does not need to be re-programmed for different sketches.

Thank you for your help. Do you know if it's possible for me to get the AT32 chip with firmware already installed on it so I can solder it to my PCB without worrying about installing the firmware myself?

Thank you for your help. Do you know if it's possible for me to get the AT32 chip with firmware already installed on it so I can solder it to my PCB without worrying about installing the firmware myself?

I doubt that enough people are building Arduino WiFi Shields from scratch to make pre-loading the firmware on an AT32 chip a practical business model. You should include an ICSP header for the AT32 in your design so you can load the firmware after you solder the board. You will probably need to learn how to build and install the AT32 firmware. Good luck with that.